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So I have a .fbx file with a model and a ton of animations for it as separate .fbx files but when I import the .fbx animation file into the scene currently with the .fbx model it imports a new armature that does the animation instead of making the model that is rigged do the animation

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    $\begingroup$ Just for reference: in case someone stumble upon this question, I have solved it with custom python script $\endgroup$ – Izzy Jul 27 '17 at 10:21
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I haven't seen a way to import just the keyframe information into Blender (granted I have not looked up how to). but what I normally do, though a bit tedious, you import all the fbx files containing the animations and delete the armature that comes with it. Blender will keep the animation data after the armature is deleted so after all the extra armatures are deleted you can select the armature you are using, go into your action editor (It's a different setting in your dope sheet window) and there should be a list of animations to choose from

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